HPC: A first AlphaFold run

In this exercise, the goal is to successfully execute an AlphaFold prediction on the HPC cluster. The steps you should take are described in the PowerPoint presentation or in a basic workflow example. These steps are specifically for usage via the web interface.

If you want to log in via SSH and go through all steps on the command line, an overview is also given in the tutorial material online:

• https://elearning.vib.be/courses/alphafold/lessons/alphafold-on-the-hpc/
• Or more concise in https://elearning.vib.be/courses/alphafold/lessons/alphafold-on-the-hpc/topic/basic-workflow-example/

To summarize, you will need to cover the following steps:

• Log in to the HPC
• Navigate to the right directory
• Create the appropriate directories
• Create/upload your FASTA file (example)
• Download the job script (link)
• Modify the job script
• Swap to the joltik cluster
• Submit the job script
• Verify its status
• Verify whether it runs and produces an output, or whether it crashes

AlphaFold experiments will often require more than 30 minutes, up to multiple hours. However, if your run does not crash in the first minutes, it is likely to succeed to the end.

Troubleshooting hints are found at https://elearning.vib.be/courses/alphafold/lessons/alphafold-on-the-hpc/topic/troubleshooting/.